6zav: Difference between revisions

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'''Unreleased structure'''


The entry 6zav is ON HOLD
==NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX)==
<StructureSection load='6zav' size='340' side='right'caption='[[6zav]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6zav]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_sp._ORS_375 Bradyrhizobium sp. ORS 375]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZAV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZAV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.19&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6zav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zav OCA], [https://pdbe.org/6zav PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zav RCSB], [https://www.ebi.ac.uk/pdbsum/6zav PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zav ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/H0SLX7_BRAS3 H0SLX7_BRAS3]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK Recently, we have identified two copies of nirK genes in several alpha-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br (2D)NiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br (2D)NiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.


Authors: Rose, S.L., Antonyuk, S.V., Sasaki, D., Yamashita, K., Hirata, K., Ueno, G., Ago, H., Eady, R.R., Tosha, T., Yamamoto, M., Hasnain, S.S.
An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.,Rose SL, Antonyuk SV, Sasaki D, Yamashita K, Hirata K, Ueno G, Ago H, Eady RR, Tosha T, Yamamoto M, Hasnain SS Sci Adv. 2021 Jan 1;7(1):eabd8523. doi: 10.1126/sciadv.abd8523. Print 2021 Jan. PMID:33523860<ref>PMID:33523860</ref>


Description: NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX)
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Sasaki, D]]
<div class="pdbe-citations 6zav" style="background-color:#fffaf0;"></div>
[[Category: Antonyuk, S.V]]
== References ==
[[Category: Rose, S.L]]
<references/>
[[Category: Eady, R.R]]
__TOC__
[[Category: Yamashita, K]]
</StructureSection>
[[Category: Yamamoto, M]]
[[Category: Bradyrhizobium sp. ORS 375]]
[[Category: Ago, H]]
[[Category: Large Structures]]
[[Category: Hirata, K]]
[[Category: Ago H]]
[[Category: Hasnain, S.S]]
[[Category: Antonyuk SV]]
[[Category: Ueno, G]]
[[Category: Eady RR]]
[[Category: Tosha, T]]
[[Category: Hasnain SS]]
[[Category: Hirata K]]
[[Category: Rose SL]]
[[Category: Sasaki D]]
[[Category: Tosha T]]
[[Category: Ueno G]]
[[Category: Yamamoto M]]
[[Category: Yamashita K]]
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